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Nest Settings

The Settings page allows you to create and edit a nest description and nest protocol, as well as manage User Keywords. Only the Owner and Admins of a nest can view its Settings page.

The Settings page is found in the top left of the page, underneath Nest Home and Activity. This link will only appear to the Owner and Admins in the nest; Settings are hidden from Users.

1. Add and Manage Admins, Users, and Organizations

Add or remove User and/or Admin privileges for individuals and access and/or Ownership for Organizations in your specific nest. To learn how to do so for individuals or organizations, see the Manage Access page.

Note: Nest-level Admin functions are separate from Organization-level Admin functions.

  • For Organization-level Admin functions, see Manage Organizations.
  • Exception: if you are giving an Organization access to or ownership of a nest, that is a Nest-level Admin function; see the Manage Access page.

2. Synthesis

From the Synthesis section, you can toggle 'on' or 'off' any Synthesis page:

  • Toggle on or off Quantitative Synthesis, Qualitative Synthesis, Dashboard, Manuscript, Critical Appraisal, or PRISMA. If toggled off, that specific subsection will be greyed out in the Synthesis homepage.

Adjust the privacy/publicity of your Synthesis page to be Public, Protected, or Private:

  • Make a nest public. Toggle this on to make the link to your Synthesis page (and all sub-pages) publicly viewable.
  • Make a nest protected. Toggle this on to make the link to Synthesis undiscoverable and inaccessible to those without the key (or explicitly granted access). You will still be able to share a link with external parties, and the external party will not have to log in to view Synthesis.
  • Make a nest private. Toggle this on for the most protection. Only those explicitly granted access with a NK account will be able to view the Synthesis.

3. Screening

Screening Modes: Standard vs. Dual vs. Two-Pass Screening

As an Admin, you can configure the Screening Mode to be:

Standard Screening means that each record will be screened by one user in a single session. The user will have the option of designating “Full Text Review”, but there is no separate Full Text step.

Dual Screening means that each record will be screened by two different users and adjudicated by a third.

Two-Pass Screening means that each record will be screened at the Abstract level by one user, and advanced to a second, separate Full Text screening step, where the record must have a full text PDF uploaded and a final Screening decision made by a single user.

Dual Two-Pass Screening combines these functions, meaning each record is screened by two different users and adjudicated at the Abstract step, and then two users must screen at the Full Text step followed by adjudication.

Toggling between Standard, Two-Pass, and Dual Screening (see image) can lead to loss of data, as only the final Inclusion and Exclusion decisions will be saved if you switch between Screening Modes!

Screening Model

Manual vs. Automatic: By default, the Screening Model will be on Manual, meaning that it will only run when a user selects Train Screening Model during the Screening process. Toggling the Screening Model on (see image above) will alter this so that the Model runs as soon as a sufficient number of studies are screened, and this Model will be re-run automatically as more screening occurs. In the image below, if manual the red box will say “Train Screening Model,” and if automatic training is on and enough studies are screened, the inclusion probability will be provided– in this case it is “P(Inclusion): 0.87.”

Displayed vs. Hidden: By default, the Screening Model will be displayed, meaning that any user will be able to see the probabilities on the Screening panel:

If you want this probability to be hidden from all users, Admins, and Owners on each individual study, toggle “Hide Probabilities.” If hidden, you can still run the model from the Admin page and have the option to turn on Automatic updating. Learn more about the Screening model here.

Import Existing Screening Decisions

If there are screening decisions from a previous nest that are relevant to your current nest, you can import existing screening decisions for any record already in your nest by uploading a spreadsheet. To do this, under Screening on the Settings page, selecting “Begin” under Import.

4. Tagging

Tagging, by default, is in Form-based mode or you can turn on Standard mode:

In this mode, your configured tags will be displayed as an open-ended list to be selected from in order to extract data.

Tag Recommendations

Standard tag recommendations are available to all users to assist in the Tagging process. Smart Tag recommendations are only available to enterprise users, but utilize OpenAI GPT 3.5/4 to search Abstracts and Full Texts. Toggling on “Smart (Beta)” will automatically generate recommendations for any included studies with available full texts. This will run in the background.

You have a limited number of regenerations due to the costliness of each generation. After full text smart recommendations are generated, and for further assistance, you have the option to also generate smart tag recommendations for included abstracts. Learn more about Tag Recommendations.

Import Existing Tags

If there are tags from a previous nest that are relevant to your current nest, you can import existing tags for any record already in your nest by uploading a spreadsheet. To do this, under Tagging on the Settings page, selecting “Begin” under Import.

5. Meta-Analytical Extraction (previously named Extraction)

MA Extraction Modes: Standard vs. Dual

As an Admin, you can configure the Meta-Analytical Extraction Mode to be:

Standard MA Extraction means that each record will be extracted for quantitative data only once.

Dual MA Extraction means that each record will be extracted by two different users and adjudicated by a third. To toggle Dual MA Extraction 'on', select it in the Admin page:

6. Critical Appraisal (previously named Risk of Bias)

Choose a Critical Appraisal system. Learn more about Configuring Critical Appraisal

7. Blinding

To avoid bias in your review where multiple reviewers are participating, you may want to consider blinding certain aspects of the process. The Blinding settings allow you turn off or hide features.

Blind Adjudication allows you hide the reviewer's identity for each decision as to not influence the ultimate decision. For example:

Adjudicate Screening before Blinding:

After Blinding:

Hiding Inclusion Model allows you to remove the inclusion probability for each study if turned on, so the reviewer can make a completely independent decision.

Screening before hiding probabilities:

After hiding probabilities:

Hiding Comments removes the Comments tab in the workflow modules (Screening, Tagging, MA Extraction, Critical Appraisal), allowing you to hide any comments made on studies when viewing them. As a result comments can't directly be made as they appear in the queue but can be made and seen when the study is accessed in Study Inspector.

Right hand side tabs before hiding comments:

After hiding comments:

Hiding Tagging During Screening removes the Tagging tab available as you screen. We offer this capability during screening to be able to apply preliminary tags, but similarly it also exposes users to bias after a previous reviewer has screened and tagged. The before and after mirrors the above Comments removal but for the Tagging tab instead in Screening alone.

8. Copying, Renaming, or Deleting a Nest

Copying a nest will copy the data and configurations, such as the search terms, references, exclusion reasons, the tagging hierarchy, applied tags, data elements, full-text PDFs, Critical Appraisal systems, the protocol and manuscript, and other configurations. The copied nest is entirely independent of the original nest. Access privileges will not be copied from the old nest and must be configured.

Only Owners have the right to delete a nest. “Delete” can be found next to “Rename”; deleting a nest is irreversible and will completely delete all data related to the project in question!

Deleting a nest has wide-reaching and irreversible effects, including loss of all nest data. Proceed with caution!

Enterprise-level Features

These features are only available to admins within an organization subscribed at the Enterprise level.

1. Allocation

Allocation allows you to assign work in specific modules to various members of your team. Learn more about Allocation.

2. Nest Backups

Nest Backups allow you to manually save up a backup of your nest to capture a version of it at a specific date and time. Learn more about Nest Backups.

wiki/autolit/admin/configure.txt · Last modified: 2023/12/06 22:06 by jthurnham